Genetic Diversity among Tropical Provitamin A Maize Inbred Lines and Implications for a Biofortification Program

Abstract

Insights into the diversity and relationships among elite breeding materials are an important component in maize improvement programs. We genotyped 63 inbred lines bred for high levels of provitamin A using 137 single nucleotide polymorphism markers. A total of 272 alleles were detected with gene diversity of 0.36. Average genetic distance was 0.36 with 56% of the pairs of lines having between 0.30 and 0.40. Eighty-six percent of the pairs of lines showed relative kinship values <0.50, which indicated that the majority of these provitamin A inbred lines were unique. Relationship pattern and population structure analysis revealed presence of seven major groups with good agreement with Neighbour Joining clustering and somewhat correlated with pedigree and breeding origin. Utilization of this set of provitamin A lines in a new biofortification program will be aided by information from both molecular-based grouping and pedigree analysis. The results should guide breeders in selecting parents for hybrid formation and testing as a short-term objective, and parents with diverse alleles for new breeding starts as a long-term objective in a provitamin A breeding program.

References

  1. Adeyemo, O., Menkir, A., Melaku, G., Omidiji, O. 2011. Genetic diversity assessment and relationship among tropical yellow endosperm maize inbred lines using SSR markers. Maydica 56:1703.

    Google Scholar 

  2. Adeyemo, O., Omidiji, O. 2014. SSR-based and carotenoid diversity assessment of tropical yellow endosperm maize inbred lines. Plant Genet. Resour.-C. 12:67–73.

    CAS  Article  Google Scholar 

  3. Azmach, G., Melaku, G., Menkir, A., Spillane, C. 2013. Marker-trait association analysis of functional gene markers for provitamin A levels across diverse tropical yellow maize inbred lines. BMC Plant Biol. 13:227.

    Article  Google Scholar 

  4. Badu-Apraku, B., Oyekunle, M., Fakorede, M.A.B., Vroh, I., O Akinwale, R., Aderounmu, M. 2013. Combining ability, heterotic patterns and genetic diversity of extra-early yellow inbreds under contrasting environments. Euphytica 192:413–433.

    CAS  Article  Google Scholar 

  5. Bradbury, P., Zhang, Z., Kroon, D., Casstevens, T., Ramdoss, Y., Buckler, E. 2007. TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23:2633–2635.

    CAS  Article  Google Scholar 

  6. Brunson, A., Quackenbush, F. 1962. Breeding corn with high provitamin A in the grain. Crop Sci. 2:344–347.

    CAS  Article  Google Scholar 

  7. Cairns, J.E., Sonder, K., Zaidi, P.H., Verhulst, N., Mahuku, G., Babu, R., Nair, S.K., Das, B., Govaerts, B., Vinayan, M.T. 2012. Maize production in a changing climate: Impacts, adaptation, and mitigation strategies. Adv. Agron. 114:1–58.

    CAS  Article  Google Scholar 

  8. Dao, A., Sanou, J., Mitchell, S.E., Gracen, V., Danquah, E.Y. 2014. Genetic diversity among INERA maize inbred lines with single nucleotide polymorphism (SNP) markers and their relationship with CIMMYT, IITA, and temperate lines. BMC Genetics 15:127.

    Article  Google Scholar 

  9. Evanno, G., Regnaut, S., Goudet, J. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecolology 14:2611–2620.

    CAS  Article  Google Scholar 

  10. Farfan, I.D.B., De La Fuente, G.N., Murray, S.C., Isakeit, T., Huang, P.-C., Warburton, M., Williams, P., Windham, G.L., Kolomiets, M. 2015. Genome wide association study for drought, aflatoxin resistance, and important agronomic traits of maize hybrids in the sub-tropics. PLoS One 10, e0117737.

    Article  Google Scholar 

  11. Fiedler, J.L., Afidra, R. 2010. Vitamin A fortification in Uganda: Comparing the feasibility, coverage, costs, and cost-effectiveness of fortifying vegetable oil and sugar. Food Nutr. Bull. 31:193–205.

    Article  Google Scholar 

  12. Hardy, O., Vekemans, X. 2002. SPAGeDi: a versatile computer program to analyse spatial genetic structure at the individual or population levels. Mol. Ecol. Notes. 2:618–620.

    Article  Google Scholar 

  13. Ligges, U., Mächler, M. 2002. Scatterplot3d – an R package for visualizing multivariate data. J. Stat. Softw. 8:1–20.

    Google Scholar 

  14. Liu, K., Muse, S.V. 2005. PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21:2128–2129.

    CAS  Article  Google Scholar 

  15. Liu, K., Goodman, M., Muse, S., Smith, J., Buckler, E., Doebley, J. 2003. Genetic structure and diversity among maize inbred lines as inferred from DNA microsatellites. Genetics 165:2117–2128.

    CAS  PubMed  Google Scholar 

  16. Lu, Y., J. Yan, C., Guimarães, S., Taba, Z., Hao, S., Gao, S., Chen, J., Li, S., Zhang, B., Vivek, C., Magorokosho, S., Mugo, D., Makumbi, S., Parentoni, T., Shah, T., Rong, J., Crouch, Y. Xu. 2009. Molecular characterization of global maize breeding germplasm based on genome-wide single nucleotide polymorphisms. Theor. Appl. Genet. 120:93–115.

    CAS  Article  Google Scholar 

  17. Melchinger, A., Lee, M., Lamkey, K., Hallauer, A., Woodman, W. 1990. Genetic diversity for restriction fragment length polymorphisms and heterosis for two diallel sets of maize inbreds. Theor. Appl. Genet. 80:488–496.

    CAS  Article  Google Scholar 

  18. Menkir, A., Maziya-Dixon, B., Mengesha, W., Rocheford, T., Alamu, E.O. 2017. Accruing genetic gain in provitamin A enrichment from harnessing diverse maize germplasm. Euphytica. 213:105.

    Article  Google Scholar 

  19. Menkir, A., Olowolafe, M.O., Ingelbrecht, I., Fawole, I., Badu-Apraku, B., Vroh, B.I. 2006. Assessment of testcross performance and genetic diversity of yellow endosperm maize lines derived from adapted × exotic backcrosses. Theor. Appl. Genet. 113:90–99.

    CAS  Article  Google Scholar 

  20. Muthusamy, V., Hossain, F., Thirunavukkarasu, N., Choudhary, M., Saha, S., Bhat, J.S., Prasanna, B.M., Gupta, H.S. 2014. Development of β-carotene rich maize hybrids through marker-assisted introgression of β-carotene hydroxylase allele. PLoS One 9:e113583.

    Article  Google Scholar 

  21. Olmos, S., Delucchi, C., Ravera, M., Negri, M., Mandolino, C., Eyhérabide, G. 2014. Genetic relatedness and population structure within the public Argentinean collection of maize inbred lines. Maydica, 59:16–31.

    Google Scholar 

  22. Pixley, K., Palacios-Rojas, N., Babu, R., Mutale, R., Surles, R., Simpungwe, E. 2013. Biofortification of maize with provitamin A carotenoids. In: S.A. Tanumihardjo (ed.), Carotenoids and Human Health, (pp. 271–292). Springer Science + Business Media, New York, NY.

    Chapter  Google Scholar 

  23. Pritchard, J., Stephens, M., Donnelly, P. (2000). Inference of population structure using multilocus genotype data. Genetics 155:945–959.

    CAS  PubMed  PubMed Central  Google Scholar 

  24. Pritchard, J., Stephens, M., Donnelly, P. 2000. Inference of population structure using multilocus genotype data. Genetics 155:945–959.

    CAS  PubMed  PubMed Central  Google Scholar 

  25. Rafalski, A. 2002. Applications of single nucleotide polymorphisms in crop genetics. Curr. Opin. Plant Biol. 5:94–100.

    CAS  Article  Google Scholar 

  26. Reif, J., Melchinger, A., Xia, X., Warburton, M., Hoisington, D., Vasal, S. 2003. Genetic distance based on simple sequence repeats and heterosis in tropical maize populations. Crop Sci. 43:1275–1282.

    Article  Google Scholar 

  27. Rogers, J.S. 1972. Measures of genetic similarity and genetic distance. In: Studies in Genetics VII, University of Texas Publication 7213, Austin, pp. 145–153.

  28. Semagn, K., Magorokosho, C., Vivek, B., Makumbi, D., Beyene, Y., Mugo, S., Prasanna, B., Warburton, M. 2012. Molecular characterization of diverse CIMMYT maize inbred lines from eastern and southern Africa using single nucleotide polymorphic markers. BMC Genomics 13:113.

    CAS  Article  Google Scholar 

  29. Sserumaga, J.P., Makumbi, D., Hyeonso, J., Kiarie, N., James, W.M., George, N.C.W., Lee, S.-M., Godfrey, A., Hakbum, K. 2014. Molecular characterization of tropical maize inbred lines using microsatellite DNA markers. Maydica 59:267–274.

    Google Scholar 

  30. Suwarno, W.B., Pixley, K.V., Palacios-Rojas, N., Kaeppler, S.M., Babu, R. 2014. Formation of heterotic groups and understanding genetic effects in a provitamin A biofortified maize breeding program. Crop Sci. 54:14–24.

    Article  Google Scholar 

  31. Suwarno, W.B., Pixley, K.V., Palacios-Rojas, N., Kaeppler, S.M., Babu, R. 2015. Genome-wide association analysis reveals new targets for carotenoid biofortification in maize. Theor. Appl. Genet. 128:851–864.

    CAS  Article  Google Scholar 

  32. Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., Kumar, S. 2011. MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28:2731–2739.

    CAS  Article  Google Scholar 

  33. Van Inghelandt, D., Melchinger, A., Lebreton, C., Stich, B. 2010. Population structure and genetic diversity in a commercial maize breeding program assessed with SSR and SNP markers. Theor. Appl. Genet. 120:1289–1299.

    Article  Google Scholar 

  34. Warburton, M.L., Xia, X.C., Crossa, J., Franco, J., Melchinger, A.E., Frisch, M., Bohn, M., Hoisington, D.A. 2002. Genetic characterization of CIMMYT maize inbred lines and open pollinated populations using large scale fingerprinting methods. Crop Science 42:1832–1840.

    Article  Google Scholar 

  35. Wen, W., Araus, J., Trushar, S., Cairns, J., Mahuku, G., Bänziger, M. 2011. Molecular characterization of a diverse maize inbred line collection and its potential utilization for stress tolerance improvement. Crop Sci. 51:2569–2581.

    Article  Google Scholar 

  36. West, K.P. Jr. 2002. Extent of vitamin A deficiency among preschool children and women of reproductive age. J. Nutr. 132:2857S–2866S.

    CAS  Article  Google Scholar 

  37. Wu, Y., San Vicente, F., Huang, K., Dhliwayo, T., Costich, D.E., Semagn, K., Sudha, N., Olsen, M., Prasanna, B.M., Zhang, X., Babu, R. 2016. Molecular characterization of CIMMYT maize inbred lines with genotyping-by-sequencing SNPs. Theor. Appl. Genet. 129:753–765.

    CAS  Article  Google Scholar 

  38. Xia, X.C., Reif, J.C., Melchinger, A.E., Frisch, M., Hoisington, D.A., Beck, D., Pixley, K., Warburton, M.L. 2005. Genetic diversity among CIMMYT maize inbred lines investigated with SSR markers. II. Subtropical, tropical mid-altitude, and highland maize inbred lines and their relationships with elite U.S. and European maize. Crop Sci. 45:2573–2582.

    CAS  Google Scholar 

Download references

Author information

Affiliations

Authors

Corresponding author

Correspondence to J. P. Sserumaga.

Additional information

Communicated by M. Taylor

Electronic supplementary material

Rights and permissions

This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Sserumaga, J.P., Makumbi, D., Warburton, M.L. et al. Genetic Diversity among Tropical Provitamin A Maize Inbred Lines and Implications for a Biofortification Program. CEREAL RESEARCH COMMUNICATIONS 47, 134–144 (2019). https://doi.org/10.1556/0806.46.2018.066

Download citation

Keywords

  • maize
  • inbred
  • SNP
  • provitamin